The Rift
by Zandra's Ashes
Summary: Post Trinity. McKay doesn’t fully understand why John and Elizabeth are so angry. John's friends try to protect him from himself when Elizabeth makes a devastating decision.
1. Chapter 1

Post Trinity. McKay seems almost surprised at the depths of Elizabeth's and John's anger over their disappointment in his actions.

Tiny excerpts from Trinity- Credit to Damian Kindler.

Disclaimer: Don't own, don't make any money from my "borrowing" of these beloved characters.

John winced when the transport door opened, the sounds of Elizabeth's screaming voice brought his exiting footsteps to a sudden stall. He grudgingly gave McKay credit for that at least, he'd started running as soon as the jumper touched down to personally issue his apology to Elizabeth. Looks like he'd made good time.

His lips pressed tightly together as he considered his options. Elizabeth was clearly busy, now obviously was _not_ a good time for John to scope out how much of her anger she held in reserves waiting to be deployed against him. He considered heading for the mess hall, figuring he'd better eat while McKay still solely enjoyed the focus of her anger. Mostly well deserved anger. John would not soon forget his role, Elizabeth's surprise at his endorsement of McKay's plan. He could still hear the chilly tone of her voice: "He really sold you, didn't he?" He'd seen the pain in her eyes.

Elizabeth's screaming voice was almost unintelligible from his distance. Then he clearly heard: "Putting your life and other people's lives at risk. You destroyed three quarters of a solar system!" John wheeled around and began moving again, plotting ways to delay his turn for her wrath for as long as possible.

After a quick stop by the mess hall and brief meeting with Lorne, John was heading back towards his quarters, dread growing with every step he took. The weight of her disappointment was weighing heavier upon his shoulders each moment he avoided facing Elizabeth.

Several crew members stopped him along the way to tell him McKay was looking for him. He wasn't surprised, John had turned off his radio long ago. He now boasted a field walkie talkie that only Lorne could reach him on in case of a true emergency. Realizing his quarters was not an appropriate shelter for a hide out, he diverted his path leading him directly into McKay.

John turned sharply on his heel and headed for the nearest transport. He cursed silently as McKay followed, wondering why the man couldn't take the hint. McKay began to prattle away, but John could hardly focus on his words. McKay would never totally understand why they were so angry. And John could hardly explain that Elizabeth's anger now had little to do with him. McKay might even be a little disappointed if he could wrap his apologetic egotistical head around the concept.

"I would hate to think that recent events might have permanently dimmed your faith in my abilities, or your trust. At the very least, I hope I can earn that back." McKay's voice punctured through John's thoughts.

He realized McKay had stopped talking and was looking at him expectantly. "That may take a while Rodney."

When the door to the transport had safely closed behind him he sighed heavily. "And that depends on how long it takes her to forgive me."

When the transport door opened again, two small hands struck his chest and shoved him back inside. John didn't say a word as Elizabeth closed the door and the transport began to move. Damn McKay! He'd be on the other side of the city by now if McKay hadn't been such a baby about tracking him down.

Elizabeth stood in front of him, her eyes firmly blazing into his own. While he'd expected her anger, expected her screaming, he wasn't prepared for this silence. Her anger extended over him like a field, locking him firmly in place. The intensity bristling from her eyes felt as though it was burning his skin. Every nerve in his body was fighting in response to the sudden heat, but John found himself powerless to even wipe the sweat that had broken out on his forehead.

She turned when the transport door opened and began briskly walking down the corridor. There was no question he was expected to follow. The crew members in the hall gave them wide clearance when they spotted Elizabeth. Her feet pounded so loudly, the crew had their backs to the wall and were now giving the pair their full attention. Elizabeth was heading straight for her quarters, apparently oblivious to the rumors that had grown rampant in recent weeks. Or just mad enough to no longer give a damn John considered watching her rigid stride. He gritted his teeth and pressed forward his thoughts filled with various techniques for killing McKay.

Elizabeth strode into her quarters, through the room, and out onto the balcony. She had never looked back, not even once since leaving the transport. He realized that McKay had not borne the brunt of her anger, the worst was obviously still to come.

John paused inside the doorway, before turning back to see every head in the hall still staring wide eyed their way. His eyes narrowed and he moved back into the hallway, turning to glare at each and every one of the staring crew members. Their footsteps couldn't scatter fast enough. John's head was still shaking back and forth as he moved into her room, firmly locking the door behind him.

TBC………………..


	2. Chapter 2

A/N: Pt. 2 of 3. Sorry for the delay, blame it on the damn mistletoe

Disclaimer: Don't own, don't make any money from my "borrowing" of these beloved characters.

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John took a deep breath as he looked at Elizabeth out on her balcony. He could see her shaking from where he stood. His heart began to beat even faster. He could leave, he briefly considered. Give her more time to calm down. He imagined her knuckles were white from the grasp she had on the balcony railing. Taking another deep breath he couldn't shake the feeling that he deserved this, he owed her the right to vent her rage upon him. They had all pushed her into it. McKay, Caldwell, himself, she'd known the test would happen no matter what she wanted. She'd been backed into saving face by approving it without force. But he couldn't pretend it had been without extreme pressure.

He saw her shaking still as he grew closer. So many things that needed to be said froze on the tip of his tongue as he remembered the taste of her kiss, remembered the feel of her arms woven tightly around him. The heat began to finally fade away from his body, replaced quickly with a painful chill. She'd finally given him a chance to let him love her and he blew it. Blew it with an explosion the size of a solar system. A dark pit began to coil in the pit of his stomach as he realized their first kiss was probably going to be their last. But she'd let them go. How was she going to blame it all on them, they may have pushed her but she said yes. Unless she'd been looking for an excuse to walk away from him.

"Just go ahead Elizabeth. We all fucked up, disappointed you and your illusions of a perfect universe. To hell with that, life is messy and unpredictable and no matter how hard you may wish otherwise it will never be a fairy tale." John knew he was pushing her further over the edge, but he no longer gave a damn.

She took a step back, her back striking the balcony rail with a thud. She didn't seem to even notice. She averted her head to the side as he moved forward. "John. I need you to go. I thought I could do this, but shit, I can't think with you around me." She was whispering now, almost as though trying to force her voice from yelling.

"Elizabeth…" He brushed his hand across her cheek but she turned the other way. He brought both hands up, cupping her chin towards him.

"John…you…need…to…go. _Now_!" Her voice had grown louder with each word and when he faltered, she shoved against his shoulders giving herself room to move away.

"Damn it Elizabeth, what are you doing!" John moved around grabbing her shoulders twisting her back around to face him. "You can't just kiss me like you did yesterday and then try to throw me out like I'm no one today. We need to talk about Doranda."

Elizabeth brought her arms up between Johns before pushing his hands outwards and freeing herself from their grip on her shoulders. "I don't want to talk about Doranda John. Why don't you understand that I can't talk to you right now?"

She turned away from him again moving back to the railing of the balcony. He caught her wrist as her hands smoothed her curls away from her eyes. He tugged her back around again. "Christ Elizabeth, I'm not doing this with you. You feel guilty, you feel like your focus was split. To hell with that. You are too damn hard on yourself."

John took a deep breath waiting, but Elizabeth remained stubbornly locked in silence. "Don't punish me for what you did to McKay. No one in Atlantis missed you screaming at him tonight, and you know he didn't deserve that. It's our job to protect McKay from himself and we failed. You know once the military on Earth got wind of this they would have made us proceed with testing. More people than I could have evacuated would have been there. You saved lives by letting him try."

"I almost got you both killed." She whispered.

"Elizabeth you kissed _me_ yesterday, you came to find _me_ tonight. You didn't have to see me at all, god knows I wasn't about to come looking for you. Finish what you started Elizabeth! Is this over? Because if so I want to hear you say it. I deserve to hear you say it." His voice had emerged in a deep angry tone, one he could never have imagined using with Elizabeth before.

But something was coursing through his veins now, like her anger had somehow rubbed off on him. But it was more than anger. It was mixing turbulently with the intense feelings he held for the woman before him, washing over him and leaving him reeling from the powerful aftershocks. He could almost taste her kiss; he could still smell the intoxicating aroma hinting about her neck. Her body was twisting away from him as he moved to pull her around to face him. She wiped again at the hair splaying against her face and he took the opportunity to snatch her hand. She swatted at him gently, and then more forcefully as he persisted.

"Damn it John, why won't you go away? I'm pissed; I don't want to say…" Elizabeth broke free and John followed her to the side railing of the balcony.

"Look at me Elizabeth!" He was beginning to feel like a wild animal as he pawed at her, pulling at her, willing her to yield. He just wanted to see her face, needed to see her eyes. "Don't want to say what Elizabeth? Convenient isn't it that I managed to piss you off so soon. Gives you the perfect excuse to change your mind about us."

She chose that moment to turn her head back to him. As he hair fell away revealing her face, John sucked in his breath when he saw her. Tears. Not hair. She'd been brushing tears away from her face. And her eyes glistened like he'd never seen them before as the tears danced upon her still furious eyes.

He held his breath as she moved forward and-"Ow! You kicked me!" John gingerly bent over to rub his throbbing knee.

"Why will you never do anything I ask? I just didn't want to say something I wouldn't regret John. Why didn't you leave?" Elizabeth moved forward again before John could straighten himself and she shoved hard against his shoulders.

John teetered off balance falling the short distance to the floor. He looked up at her wanting to reach out to her so badly, but not wanting to push her further. Though his timing sucked, he couldn't stop the laughter bubbling through his chest from escaping. Elizabeth Weir had just kicked his shin. He had a random flashback to grade school and a little brunette with the longest curly hair. He never could resist pulling it.

Elizabeth bent over him, her anger softening as a concerned look flashed over her eyes. He reached up to touch a curling tendril of hair dancing down towards him. She smacked his hand away. "Looks like you'll live."

He grabbed her hand as it pulled back, grasped the small of her back and pulled her firmly down towards him.

"John stop it!"

He could hear her tone lighten as if she was trying to suppress her own laughter now. Didn't mean she still wasn't mad he quickly found. Elizabeth fought like hell to escape his grasp. His continuing laughter was clearly not helping her mood. She made a last ditch effort to twist away and John turned with her, pinning her now with her back to the floor as his body stretched over hers.

He looked down at her tear dampened face that was still fighting to control the corners of her lips threatening to turn upward. His laughter fell flat as their eyes found each others. Elizabeth's body stilled as they stared into each other's eyes.

"Elizabeth, I'm not going anywhere. Not today, not tomorrow, not ever. Don't waste your beautiful pout trying to force me to do anything different." He said, somewhat shocked to hear the words almost flawlessly escape his mouth. Maybe all that emotional stuff wasn't so hard after all, if you had the right person.

She was still focused on his eyes, searching intently to her unasked questions. He could still feel the heat pooling off her body and almost see her struggle to relinquish her safety net of anger.

"You came looking for me tonight Elizabeth-"

She rolled away from him. The tears had all but dried from her face, but her eyes bespoke a different story. They looked anguished. He moved quickly to his knees but she moved away again standing briskly before turning her back to him.

"If I can't control the expedition, I have no right to be here. Maybe I never did. _That _is one of the few mistakes I have the power to correct." Elizabeth's voice was quaking.

"Don't." Fear gripped John's heart as he watched Elizabeth's frighteningly still body. "Elizabeth I know what you are thinking, you can't, I won't allow it!" John stood up behind her. The second his fingertips brushed her shoulder she was moving.

"I can't stop you from trying to stop me. _ I_ obviously can't make you do anything. But at some point, I have to take a stand. And I have to do so before I allow anyone else to get killed under my watch. If you won't leave, I will." She slipped out the doorway and John could only watch in shock.

A/N: Again, this is part 2 of 3. Sorry for any grammatical errors, this was edited quickly and without beta. Forgive me


	3. Chapter 3

"Sheppard! What the hell did you do? Weir's trying to resign her post." Jack O'Neil's pissed off voice couldn't be suppressed even as it travelled galaxies to reach John's ears.

"Sir?"

"Don't play dumb with me Sheppard; I saw her looking at your messy head with those big doe eyes of hers. You were like the grand finale at the 4th of July fireworks when you sat down in that chair in Antarctica. I told you not to touch anything!"

John felt like he'd been kicked in the gut. "She resigned."

"What- did you get hit in the head recently? Let's get it together Sheppard."

John rubbed his hands over his face. He didn't think she'd go through with it, didn't think she'd do something so rash so quickly. She'd done it on purpose he realized, done it before even giving him a chance to talk her out of it. He'd been looking for her since last night, constantly until the moment Chuck called him to the control room for this "conference call" with General O'Neil.

"Sheppard, I'm talking here and you're not paying a damn bit of attention. You listening yet?"

"Sorry sir." John blinked wondering how long he'd withdrawn to his thoughts. "Yes sir, I'm listening."

"You want her to leave?" Jack asked, blunt as his usual charming self could be.

John pressed his eyes together, turning his head away from the monitor before him.

Jack's voice rattled away. "Chuck, get out of there I know you're hovering. Walter, take a break."

John focused on his breathing, barely noticing that Jack was effectively clearing both of their rooms so they could speak in private.

"Sheppard, I can only do so much from here. I told her I only accept resignations one day a year. That day was yesterday so she'll have to wait. She wasn't too happy about that."

"I'll bet." John said, barely realizing he'd spoken aloud.

"What the hell did you do? You'd think you'd blown up a galaxy or something."

John winced visibly.

"Sheppard, you didn't."

"No, but it might have been close to the size of a solar system."

"You really have a knack for taking people's breath away, you know that right?" Jack turned his head from side to side as though ensuring no one was listening. "Look. I've heard…talk. I know what it's like to work together and feel…more than you're supposed to for co-workers. Don't let that stop you."

"Sir?"

"For Christ's sakes John, kiss her already." O'Neil hissed.

"Been there, done that."

"Are you sure you're doing it right?"

John's head turned along with his rolling eyes. "Hasn't seemed to be a problem before sir."

"Well try again! And stop blowing up solar systems! I'll expect a full report of your progress in one week. Sheppard, Carter's tapped to be a replacement if Elizabeth ever leaves."

"Yes sir, she would be an excellent choice I'm sure."

"Sheppard, I will personally see to it that your life becomes a living hell if Sam ends up in the Pegasus galaxy. Like I said, I know what it's like to feel more than I'm supposed to for my co-workers. One week." The screen went dead before him.

John had been trying to catch up with Elizabeth since his feet finally obeyed his commands to move. That had taken almost five minutes after Elizabeth left the night before. One week might not give him enough time to even find her at the rate he was going. Sighing, he rose to his feet. He was going to need some help, and the help he needed, well…He needed to do some damage control with his relationship with McKay anyway.

A/N. Hmm… so shoot me, I was wrong. This is obviously not the end, so how 'bout this time I just say…TBC


	4. Chapter 4

"You're kidding, right? Sheppard, scaring me like that is a lousy thing to do just because you're mad at me." McKay turned his head as he considered the ramifications. "Can you just imagine if Elizabeth did resign? We both know we'd end up with a military leader, which is problematic for several reasons but mostly because I tend to say whatever's on my mind which includes telling them when they are being stupid. And wrong. I'd end up tucked away in Area 51 or someplace worse, like McMurdo."

John slanted his eyes at Rodney and silently counted to ten. Yelling at Rodney now would hardly be productive

"You're not joking are you?" McKay's face drained of color. "This is because of me, because of Doranda?" He whispered.

"No McKay. Because of me." John lowered his head, barely peeking his eyes up to see if Rodney had understood.

"But I asked you to trust me, I knew Elizabeth-"

John kept his head down and shoved his fists deep into his pockets. "Rodney. This has nothing to do with you blowing up a solar system."

McKay held up a finger, waggling it rapidly. "Actually John it wasn't an_ entire_ solar system."

John's head snapped up. "McKay!"

"Right, sorry. All right, can we start over? _Why_ exactly is Elizabeth resigning? What did you do?"

John pressed his lips together as he swiveled away from Rodney. He ran his fingers through the back of his hair, stalling.

"Ohhh."

McKay sucked in his breath so quickly John almost wished they were outdoors. McKay probably would have inhaled an ample amount of insects.

McKay quickly recovered but was almost whispering when he started speaking again. "_You._ And Elizabeth…"

John stood with his back to McKay; he could only slightly shrug his shoulders in response.

McKay cursed under his breath. "It figures; I owe Zelenka money! I thought it would take you two a lot longer to cave-"

"McKay!" John spun around, his eyes burning.

"Right, sorry." McKay was tapping his chin thoughtfully. "So it wasn't that I blew up a solar system, she was mad that _you_ sided with _me_."

"I thought it wasn't an entire solar system." John snipped, not entirely happy that he was having this conversation with Rodney. Men weren't supposed to talk about things like feelings or relationships. Hell, as a general rule John was uncomfortable even acknowledging to himself he even had emotions. Maybe he should have gone to Teyla first.

"I asked you to trust me and you did. You went against Elizabeth's judgment and you…and Elizabeth. Oh John. I'm strangely touched."

John twisted uncomfortably. "Don't let it go to your head Rodney."

"No wonder she's so mad, John what the hell were you thinking?

"Hey, what happened to Mr. "I'm touched" Rodney?"

"Yes, well I'm not stupid. Though I may have been wrong, you may not be a Kirk after all. Kirk would know better than to publicly side against his woman; that was not a very suave move. You have to be subtle, discreet. Find ways to make them do what you want while making think it had been their idea all along. What are we going to do?"

John gritted his teeth, wondering briefly how it was he hadn't killed McKay a long time ago. "First of all, it might help if I could find her!" John nodded Rodney toward the computer.

"And then what?" McKay asked as his fingers went to work, pulling up life sign readings throughout the city.

"Well…I haven't exactly figured that out yet, but O'Neil is pissed. Carter will be packing her backs for Pegasus if Elizabeth doesn't change her mind. If that scenario plays out, the General has promised to make my life a living hell."

"Hmm, Samantha? Really?" Rodney's face assumed a dreamy look of bliss.

John whacked McKay across the back of his head.

"Ow! Err, sorry. " McKay tapped his fingers on the monitor. "Well, someone is in Elizabeth's quarters. That would be an obvious place to start."

John made a break for the door.

"John, what are you going to do?" McKay's voice called behind him as John eased into a run.

Hopefully, he would figure that out. Quickly.

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A/N: TBC- Thanks for the reviews and story alerts! I hope you enjoyed!


	5. Chapter 5

_I have to warn you, I've heard relationships based on intense experiences never work._

Speed (1994)

A/N: If you are looking for fluff and fun this New Year's Eve, save this chapter for another day. Also, I am terrible at judging the rating thing. If the language or situations merit an M rating, I will be grateful if you let me know.

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John used his overrides to enter Elizabeth's quarters, figuring she wouldn't willingly let him in. The room was dark, eerily quiet. He wondered if she'd gotten one of the scientists to rig some sort of tracking device for _him_, so she'd know when he was growing near. As the lights rose, John began blinking rapidly as he focused on the room before him. This was _not_ happening. Each time he blinked, he hoped the illusion would clear from his eyes.

Everywhere he looked were boxes, piles and piles of packed boxes. She had obviously been busy. His mouth clamped together as he threw his hand against the side of a nearby box. Its contents went tumbling, scattering clothing across the floor. It was strangely satisfying to get a sense of life within her quarters again, the presence of her. The smell of her soft perfume dusted against his nose.

He grabbed another box, throwing it hard against the wall. A pile of books flew out of the box, slamming against the floor. She belonged here. Another box went flying. A previous version of herself had sacrificed her life, waiting ten thousand years to save their expedition from death. Another box sailed into the air. Maybe a better man then he could be nobler, but he refused to walk away in her place. She would have to learn to deal with him, find a way to work with him. Another box went airborne and loose sheets of paper fell like snow around him.

He struck the wall with his palm, barely recognizing the agonizing noise that escaped his throat. Atlantis flowed through him in a way he'd never dared explaining to the others. It was part of him, a part he could never turn his back on. He tossed another box and suddenly darkness fell over the room.

"What the…John!" Light suddenly hammered his eyes and he found Elizabeth before him, tugging the bra from across his face. He growled when he noticed a lacy black thong draping her shoulder, channeling his frustration by tossing another box. More books, several pelting against his side as they rained down from his hands. Her hands were behind him tugging against his shoulders but he was immersed in a black fog that had no hope of clearing until every box in her quarters had been emptied.

"John, please!" Elizabeth's voice was almost begging.

He forced his body to still somehow, but didn't dare turn around to face her. Emotions and instincts had wrenched the power of logic away from his control, just like when he was infected with the retrovirus. Just like when he'd _hurt her_. She'd recognize the danger within his eyes. His chest heaved up and down, his senses seemed to be firing on overdrive. His skin prickled uncomfortably as he drew in a deep breath of her essence. His heart drummed more erratically and John realized he needed to leave.

Slowly he forced his feet around meeting her tear laden eyes. Then he couldn't breathe at all. She pushed forward into him, his back striking the wall as her lips pushed against his. His hands trailed from her shoulders down her spine, as he somehow yielded control to the delicious demands of her mouth. He longed to yank her closer so he could lay claim to every inch of her body, making it impossible for her ever to forget she belonged to him, as he was hers. Waves of need and want flowed through his veins, dragging him closer towards the edge of the fragile bit of control left within him. She grabbed his belt loops pulling her lower body agonizingly close to his own. He groaned as he tried to still his hands, fighting desperately to stay in control.

Then she growled, sounding like a wounded animal and she shoved her hands against his hips, tearing herself away. "Shit! I can't do this John."

"Elizabeth wait!" John grabbed for her but she slipped through his fingers. He snatched again at her arm as she twisted sideways, but instead his fingers firmly grasped her shirt, ripping the seam of the left side.

"John!" Elizabeth gasped, clutching her shirt together as she opened the door and fled.

Damn it! John's knuckles cracked against the wall, the pain shocking him back to reality. She couldn't be seen in the halls with a tear stained face and a ripped shirt. They would think…he caught a glimpse of her room as he went after her. What _had _he done? John blindly crashed into McKay.

"Jesus Sheppard!" McKay's eyes stretched wide enough to burst as they moved from Elizabeth's disheveled appearance back to the destruction of her quarters.

John followed his eyes. It looked like a fucking tornado had ripped through the room. Clothing, books, papers and other personal affects covered every surface in the room.

"McKay." John took a deep breath, trying to get some sort of grasp on his emotions. "Step aside."

McKay took another look at the room behind John. "Oh, I don't think so. At the rate you are going O'Neil will turn Atlantis into the first intergalactic trash dump within a week. You." He roughly grabbed John's chin, pulling his attention away from Elizabeth's fleeing body, surprising him with the force. "You are not to go anywhere near Elizabeth. Go find Ronan or Teyla, you need to burn some of this…anger, passion, whatever you kids are calling it these days. You will not make a single move to see Elizabeth, speak to Elizabeth or even get in her line of sight unless I approve it. Go spar, I'm calling for reinforcements."

John stood in a shocked stupor of anger. He was fighting to listen to McKay, who was right incidentally. John wasn't in any shape to try to make things right with Elizabeth now. But he couldn't let her leave like this, he needed to check on her, make sure…damn it! He really was a screw up. She should have left him back at McMurdo.

"Zelenka, are you near a computer?" Rodney paused for response as his listened to his radio. "Yes, I suppose that is a stupid question. I need you to track a life sign. Corridor B outside Elizabeth's quarters, you should see one moving rapidly. Don't let it out of your sight. I need to …check on that individual, make sure they're okay. I'm going to send…" He looked at John.

"Teyla. " John pressed his eyes shut as he turned against the corridor hallway. His forehead leaned against the wall, his palms lay flat against the cold steel, allowing Atlantis to assume some of his distraught. The lights in the corridor flickered briefly and John pulled away feeling suddenly sobered.

McKay looked at him strangely. "Zelenka I'll have Teyla contact you. Just don't lose that life sign!" He was still eying John warily as he stepped away to contact Teyla.

John was pacing rapidly when McKay had finished. "What are you going to do?" Though his thoughts had cleared, John's chest was still heaving, adrenaline throbbing through his body with every beat of his heart. He couldn't just do nothing, McKay had to realize that.

"I'm going to see Carson." McKay said as if it were the most obvious thing in the world.

"I didn't hurt her Rodney."

"I know that John, but Carson can help us. He must know something useful. He's tamed Cadman and trust me," Rodney tapped his head earnestly, "I know how irrational _that_ _one_ is."

McKay headed down the hallway, only making it a few steps before he doubled back towards John. He tapped his chin thoughtfully. "I'm sending Lorne to watch you. Carson is going to instruct him that because of medical reasons, he'll be in charge of monitoring your movements, approving your activities through me. Don't even try to fight it, as soon as I tell Carson what O'Neil has threatened and that Elizabeth is trying to leave you won't stand a chance against us."

"I-" John stopped short, realizing he shouldn't push. Hell, if McKay told anyone but Carson what had happened here, John would be destined for the brig and another court marshal.

McKay looked again into Elizabeth's quarters shaking his head in disbelief. "You screwed up John. I'll admit you had a lot of help from the rest of us along the way. In our defense, we didn't know that you…and Elizabeth..." McKay sighed, a sad smile creeping across his face. "Anyway, you're obviously going to need our help. We're not going to let you take Atlantis down with you."

John was staring down the hallway in the direction Elizabeth had disappeared.

"John, are you even listening?" McKay rolled his eyes in frustration.

John had heard every word he said; he knew he didn't have the energy to fight them all. Truth be known, he'd take all the help he could get now. But he wasn't ready to give Rodney the pleasure. "Sorry, you were saying?"

McKay rolled his eyes again, tossing up his hands in frustration. "Go work it off. Then report back to me. _No Elizabeth! _Can you handle _that_?"

John tapped the radio beside his ear. "Ronon. Meet me in the gym. Apparently I need to spar." He glared at McKay.

"Sure. You okay?" Ronon's gruff voice responded.

"No. No… I'm not. "

"On my way."

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A/N: Sometimes you have to experience darkness before you can truly appreciate the light. TBC…


	6. Chapter 6

John felt like hell after sparing with Ronon. Now, the outside of his body hurt as much as the inside. He stepped out of the gym's showers and swiped a towel against the steamy mirror. He wasn't too surprised to discover he also looked like hell. The steam crept comfortingly back across the mirror. Embarrassment over his destruction of Elizabeth's quarters had set in and he understood why Elizabeth had avoided him the day before. He could hardly look at himself after acting so foolishly.

This thought spurred more relief than his entire sparing session with Ronon; he felt strangely more at peace than since he first heard the term Project Arcturus. Maybe Elizabeth had felt just as foolish after her emotional outbursts. Fleeing Atlantis was a pretty damn permanent fix to that. He quickly toweled off and dressed. He paused to scour the top of his head with the towel before tossing it aside.

Taking a deep breath he returned to where Ronon and Lorne waited."What's the word from _Master Rodney_?"

Ronon had been filled in, courtesy of McKay. Lorne twisted uncomfortably every time he spoke to McKay on the radio and winced each time John sarcastically called McKay "Master." John figured Lorne probably knew enough at this point to realize he didn't want to be burdened with any more information.

"Sir, McKay and Carson are in complete agreement. Elizabeth will be "distracted" until we are finished." Lorne stood ready to dutifully tag along.

"All right, let's get moving. Ronon?" John hated to ask, but he wasn't looking forward to facing this task alone.

"Oh, I definitely want to see this."

Several minutes later the three men stood within the threshold to Elizabeth's quarters. John didn't dare look at either man's face, though he felt somewhat better when Ronon moved before him, smiling approvingly.

"Nice." He nodded.

John cocked his head sideways as he shrugged his shoulders. He should have known of all people Ronon would understand _this_.

"I know I'm going to regret this, but I've got to ask. Had Elizabeth packed? I know we've found nicer quarters recently, but as much time as she spends in her office it doesn't seem worth the effort. Unless she was leaving? "Lorne finally dared to look at John. "The IOA?"

John felt his face scrunching as he twisted uncomfortably. "Well…It was more of a personal issue."

Lorne looked strangely at him. "Hmm. I hope you weren't planning to repack these boxes. I think she deserves to be properly unpacked." He scanned the quarters that lay in disarray before them. "We should definitely hide the boxes."

John smiled approvingly. "I like the way you think Major. You're going to help me_, right_?" It wasn't an order because he really didn't have a leg to stand on with these two. But they'd all been through too much together to even require a demand. It wasn't a way anyone would want to spend an afternoon- and it would take that long- but soon the three men were soon elbow deep in the disarray of Elizabeth's personal effects.

A few hours later they stood near the doorway studying their work. They had transformed the near warzone into…well, actually it looked more like a bordello than anything now. None of the men had felt the courage to touch any of Elizabeth's unmentionables, so lingerie was still scattered across the otherwise pristine room. John pressed his lips together wondering if they should just leave them. He couldn't decide if Elizabeth would be so happy to find her room clean again once she realized all their grubby paws had handled her bras and panties.

"Col. Sheppard, I see you have been busy."

John had never been so happy to hear Teyla's voice. "You know, you have exquisite timing Teyla."

Teyla surveyed the room before her and smiled. She swept into the room and began gathering the remaining items like they were socks. "I can not imagine what would make you say that. I must admit, after Rodney contacted me I was quite concerned about Elizabeth."

"Yes, how is Elizabeth?" McKay's voice rang from the hallway. Carson entered the room beside him.

Teyla looked at John, a heartbreaking expression of tenderness upon her face. "I am sorry I felt concern; I had no doubt. I know you wouldn't hurt her. But when I saw her-"

"She's okay, right?" John had been waiting for hours to make sure Elizabeth was okay. Emotionally. He hoped the others realized he could never hurt her. At least when he hadn't been genetically altered by the retrovirus.

Teyla's soft laughter surprised him. "I do not know that I could say that John. She is very upset- at herself. It was quite interesting actually to hear her describe some of her recent activities involving you."

"What are you going on about? Rodney said he destroyed her room, her shirt was ripped. She's mad at herself?" Carson turned to McKay. "It could be shock."

"Carson, I never said he hurt her. She was upset. _ He_ was more upset. I knew he didn't hurt her, but he wasn't doing himself a whole lot of good with whatever game plan he had to keep her in Atlantis. She's our friend too, she was upset and I felt a responsibility to make sure she didn't do something stupid." McKay looked at John. "The same way I did with this one."

"Rodney, I'm strangely touched." John smirked.

"Really? Well, don't let it go to your head." McKay smiled at him warmly, before completely forgetting about him as he earnestly turned back to Teyla. "Exactly what were some of these recent activities?"

"Rodney!" John thrust his hands deep inside his pockets. Otherwise a fist would have certainly struck a wall and Atlantis was already unhappy with him.

"Oh come on, we've seen all the dirty laundry." McKay's eyes glanced at Teyla who was rapidly and efficiently tucking away Elizabeth's things. "Err, clean laundry. We want the whole scoop!"

"Ok _Jimmy_, been watching too many Superman movies? This is none of your business!" John looked at Lorne who seemed suddenly primed and ready for the headlines, ignorance is bliss be damned.

"Well," Teyla paused smiling upon them all, "Apparently within one solar day Elizabeth had kissed _him,_ kicked him, and pushed him to the floor before running and hiding from him. Then she kissed him again- after she saw what he did to her quarters. I think she may have mentioned shoving him again after that. "

Carson's mouth was gaping open and McKay and Lorne seemed to be choking as they tried to hold in their laughter.

"Go ahead, laugh, I'll remember this you know. I just wanted to talk to her; she kept kissing me and running away! I was trying to stop her, I wasn't attacking her. It's not my fault if she chose a flimsy shirt today. Is it?" John's mouth scrunched sideways as he pondered that thought.

"This is good then, isn't it?" Carson said.

"How is this in any way a good thing Carson?" McKay turned his best I'm smarter than you can ever hope to be face upon him.

"Isn't it obvious Rodney? She's mad at_ herself_; she's being too hard on herself. In her position, I can't imagine a single one of us wouldn't do the same. She's willing to sacrifice what she wants," Carson finally met John's eyes, smiling sadly, "sacrifice gifts she's found within her friends because her conscience can't reconcile the conflict of interest. She's already slipped with that one, hasn't she? She let herself be talked into something she didn't want and took her anger at herself out on you John…and upon you Rodney. We all heard _that_."

"Yes, well who exactly is distracting her now?" John realized everyone that _knew _was standing before him.

"Zelenka has been watching her life sign; Teyla said Elizabeth wanted to take a walk."

A deep breath John hadn't realized he'd been holding in exploded as he turned and pressed his hands against the wall. The lights flickered in Elizabeth's quarters and John pulled away feeling as though he'd been shocked.

"That- did you see that?" McKay asked. "That's what had me so worried earlier. That's the second time today I saw lights flicker when he touched the wall.

John was looking at his hands in shock. He usually couldn't understand, but now it was undeniably clear. "Elizabeth!" He started running.

"What are you doing? Did I give you permission to go anywhere?" McKay stormed after John.

John paused in the middle of the hallway, wondering if his eyes could even begin to explain everything he would never try to. "Let's go, she's in pain!" John swiveled on his heel and started running to the nearest transport.

"Who's in pain? Should we send a medical team?" Carson had joined all the others following his footsteps.

"Yes. She's in a lab; in the room we found her other self in the stasis pod." John waved the door for the transport.

"Elizabeth?" Carson asked as he stepped inside.

The door slammed shut with them all inside.

"John, is it Elizabeth?" Teyla asked.

John leaned closer to the wall before pushing his hand against it as if for support. "Carson, tell them to hurry." He whispered.

TBC…


	7. Chapter 7

Elizabeth was bent over a control panel, her open palms placed against the monitor for support. She was paler than John could ever remember seeing her as he raced to her side. He heard the footsteps of the others stall when he entered the room. John moved behind Elizabeth tucking his hand across her stomach to support her as he prepared to take her pain. He leaned forward and placed his free hand beside hers on the panel.

_Just relax, we will help. _John felt Elizabeth's body slump against his back, allowing him to help her.

_I just touched the wall, just outside the stasis pod where she had stayed. Something clamped down against my hand, injecting me. _

John hand supporting her moved to rub Elizabeth's wrist absentmindedly.

"Look at her wrist," Carson whispered, "it looks like it has been punctured.

"She'll be fine Carson, we just need to get her to the infirmary, let her rest." John said. His nose was deep within the curls of Elizabeth's hair.

"Col. Sheppard, the medical team is here, we need to-"

"Wait." John hissed. Atlantis hadn't finished, she still felt the discomfort.

"John?" Elizabeth whispered. "I can't, I need you to…"

John scooped her up as she fell, preventing her from striking the floor. Her body had fallen limp under the stress of what Atlantis had given to her. He breezed his hand against the nearby wall, hissing out a deep breath as he realized she finally had been relieved of her pain. He was aware of the others eyes upon them, wondering if they had any idea of what they had just witnessed. He looked down at Elizabeth who rested peacefully in unconsciousness. Telling them would be her call he decided. He moved into the hallway and into the transport, ignoring most of the voices against his ears. Elizabeth was somehow helping him, he was understanding much more than he could normally when he allowed himself to listen.

"Col. Sheppard, you must let her go." Carson was pulling his arms away from Elizabeth as he placed her in the mobile version of the infirmary bed.

John ignored them, crawling into the bed beside her and holding her aware that even unconscious her hands were somehow gripping him tightly in return. _You will feel better soon._

Elizabeth's voice assured him_. I never knew, John. I feel incredible and yet so..._

John looked at Carson, realizing the doctor had been oblivious to her words. As were the rest of the Atlantis crew around them.

_John, I'm so sleepy._

_Rest Elizabeth, just rest. We'll figure the rest out later._

After reaching the infirmary, John had allowed them to scrape his hands from their grasp on Elizabeth. She had still not awoken and he was now as nervous as the others. Atlantis had sensed no pain, she had indicated no pain. And yet she had not awoken. He couldn't imagine that to be a good thing. Atlantis couldn't help him with this; he never understood what it tried to tell him anyway. Only in those brief moments, had Elizabeth somehow managed to translate for him.

"Col. Sheppard?" Carson drew him away from the others. "The results are back, she seems fine, I would expect her to awaken at any moment. "

"But?" John could see Carson was holding something back.

"It's the strangest thing; her DNA is somehow binding with the ATA gene. The occurrence of this gene if the pattern continues…" Carson paused looking at Elizabeth.

"Carson." John pulled his attention back.

"If it continues in this pattern, the strength of her ATA gene will be as strong as yours, if not stronger. And that's not all."

"Just tell me Carson."

"Shortly after we arrived on Atlantis, I detected an abnormal amount of activity in one of the sections of your brain. After a few months, it stabilized and has remained unchanged and hasn't appeared to affect you or cause any harm. I now detect a similar burst within her scans. I think her puncture wound was Atlantis's version of the gene therapy. It couldn't be a coincidence it was Elizabeth who was punctured in the lab with the stasis pod. It wouldn't be a stretch to imagine Janus would prepare for this, have Atlantis help Elizabeth use all of its technology. Even if it didn't manage to happen for 10,000 years. Maybe that was his intent come to think of it. Maybe he had this ready for Elizabeth."

John frowned knowing better. Atlantis had missed her. It had drawn her there, ready to reconnect with its only friend for 10,000 years. Somehow Atlantis had made this happen.

_John?_

_I'm here. _John ignored Carson who was still formulating ideas.

_Don't leave me._

_I already told you, you couldn't make me, no matter how hard you try._

John moved closer lacing the fingers on one hand through one of Elizabeth's. The other hand he placed against the wall. The lights flickered and Elizabeth's eyes blinked open sleepily.

"How?" Her voice was raspy.

"Shush. Rest. We'll figure it out later." John squeezed Elizabeth's hand.

_John? I'm sorry._

_Me too Lizzie, me too._

_John? I'm going to kick you if you call me Lizzie again._

_Looking forward to it…Lizzie._

John brushed his fingers through Elizabeth's hair as she faded again. Smiling and looking forward to the coming days. He'd had a long time to figure out how to block this all, but she would be vulnerable. He'd be able to read her like an open book. If she hadn't already kicked him and shoved him, kissed him too, it might not be so amusing. But he was thoroughly looking forward to eavesdropping. If he hadn't cleaned up her room, he might not be deserving of such amusements, but he had tried to redeem himself, right his wrongs. She had no idea what awaited her. It was probably better that way, John decided. Otherwise, she might never open her eyes.

------

TBC….


	8. Chapter 8

A few days later, Elizabeth resumed control of her duties. She was sitting in her first staff meeting with John's team. John was blatantly tormenting Elizabeth who was striving to concentrate on the meeting around them.

_Stop it!_ She hissed.

_I have no idea what you're talking about._ John smiled towards her.

McKay was prattling about a new technique he'd devised to save energy on the puddle jumpers force fields.

John's teeth vibrated as Atlantis hummed beneath his fingertips. Elizabeth almost laughed as she looked at him._ John, it's drawing in energy from atmospheric disturbances._

_Oh, _that's _what that means. That makes more sense._

She raised an eyebrow towards him_. Why, what did you think it meant?_

_Well….._

_John!_

He shrugged, _I don't understand Ancient, you know. _Noticing Carson's intent gaze falling upon him John straightened. "Sorry McKay, what was that last part?"

Carson and McKay exchanged a slight glance that just barely registered on John's radar. He was still more focused on listening in on Elizabeth's thoughts, or what he could manage to capture of them. After months of blocking out his link to Atlantis, he'd grown somewhat rusty. He could always hear what Elizabeth intentionally shared with him, but the eavesdropping had been far from the productive endeavor he'd hoped it would be.

He looked at her red shirt, wondering if she'd left it unzipped another inch just to torment him. He was peering closer and closer to her chest.

_John! Stop it!_

_What? I'm not doing anything?_

_Really? Then maybe you could divert your eyes away from my chest!_

_Well maybe you could zip your shirt up a bit more appropriately; do you know how many men are in here now?_

_Like they are really worried about how high my shirt is zipped._

_Trust me, I'm a man, I know these things._

_Really John, you need to grow up!_

_Oh, Lizzie you don't want to point fingers, I remember a certain woman kicking my shin-_

_Yeah, and I remember a certain flyboy trashing my quarters._

_Elizabeth, this isn't the time, I've tried to talk to you-_

_John, I don't want to talk about it yet._

_Yet, here we are, again. We can't ignore it Elizabeth anymore than we can ignore this._

_Oh, I think we're doing just fine._

John looked around the room when Elizabeth jumped up turning her back to him. He noticed the others had all fallen silent watching them intently.

"Are you two ready to tell us just what the bloody hell is going on?" Carson stood to his feet. "Because I've grown a bit tired of watching you two argue without saying a word."

"Yes, to be honest, that staring bit you two do _has_ crossed over into the twilight zone territory. There is definitely more going on than you've let onto." McKay protested.

John's teeth pressed down against his lip. _See Lizzie, you're doing a crappy job of dealing with this._

_Me? You're the one who won't leave me alone! Give me a minute to adjust before you start talking my ear off and maybe we'd stand a chance._ She started pacing as John rose to his feet.

John and Elizabeth both turned leaning forward and resting their hands upon the opposite walls of the room. Oh shit. _Atlantis is pissed at both of now, do you feel that? _John turned his head back toward her.

_This is not my fault John; I'm still new at this. You could be more help you know_! She turned to glare at him.

The lights flickered and John felt a jolt of pain rip through his veins. Oh shit. He heard Elizabeth's thoughts echo his own. They turned to each other and then blackness fell across John's eyes.

"John, what-"Elizabeth's voice faded along with the light.

Carson ran towards Elizabeth as Teyla grabbed John's wrist feeling for his pulse. Elizabeth and John had both just collapsed before their eyes.

"What the hell just happened here Carson?" Rodney breathed.

"Think we finally saw a lover's quarrel, though I'm not sure either of them was victorious. " Carson looked dazed.

"How is that even possible? They never said a word." Ronan's eyes stretched painfully at he looked back and forth between John and Elizabeth.

"Aye, well that's what we'll have to find out. Once they're both conscious again anyway. Let's get them to the infirmary." Carson tapped his radio and called for a medical team.

TBC…


	9. Chapter 9

Chapter 9

McKay entered the infirmary tapping thoughtfully on his computer. He glanced over and spotted John and Elizabeth asleep on the far side of the room. Ambling up to Carson's workstation, he peered over his shoulders almost amused to find Carson muttering under his breath.

"I see your charges are behaving themselves. I guess it helps that they're sleeping." McKay edged in closer tapping at the middle monitor. "What's that?"

"I've been studying the gene therapy that Elizabeth was given, I'd hoped it would be one I could copy and work into a new process for the others in our crew who have been unresponsive."

"Carson, do you think you could use it with those who have successfully had the gene therapy? "

"Still jealous your gene isn't as strong as Sheppard's? Don't get your hopes up Rodney; I don't think I can use this on anyone, at least not for a long time. It's almost as though it was specifically developed for Elizabeth's DNA. It's quite amazing actually, you can see the-"

The monitors surrounding that screen started beeping loudly. Blood pressure and heart rates were rising simultaneously in both John and Elizabeth.

"Would you two cut it out! I'm going to sedate you both if this bickering doesn't stop!" Carson bellowed.

McKay scooted back, his ears ringing in protest. "You didn't have to yell. _Who _exactly are you yelling at by the way?"

Carson stood up glaring in John and Elizabeth's direction.

"But they're asleep." McKay peeked back at the monitors and saw the numbers dropping steadily. "They're not asleep are they?"

"No and they've been at it all afternoon. They think I won't notice, but with the monitors I couldn't ignore them if I tried. And I've tried, believe me."

"Hey Doc, will you get Elizabeth some aspirin? She gets real grouchy when her head hurts." John called out. A moment later he was chuckling softly.

McKay was relived. "He's laughing, that's good right?"

"Not so much." Carson pointed to Elizabeth's readings which were steadily rising as John's laughter continued. "Don't make me separate you two! Colonel, she needs to rest."

"Sorry Doc." John's tone was still mischievous, but he squirmed around and settled deeper into the pillow.

"Well have they told you anything yet? How does it work? Do they have to be in the same room?"

"Elizabeth doesn't want to talk about it. She said she wanted to rest first."

"Doesn't look like _that's_ going to happen anytime soon. Carson, do you have any idea how this has happened? Do they have to be touching something ancient? Is it because of the strength of their gene?" McKay leaned closer as Carson flipped through slides on the middle monitor. "We should have pushed Sheppard more about how he knew Elizabeth was in the lab that day. I checked the radio transmissions, you know, there was no anonymous call from a concerned citizen. I can't believe he thought we'd buy that."

"I'm not entirely sure about any of this yet. You're right, we should have pushed him, but I've had my suspicions about Sheppard for a while. Here, do you see this? After we arrived I noticed an abnormal amount of activity in this section of his brain."

"Carson, you will only feed my sarcasm with remarks like that. Do you know how many jokes I could…never mind." McKay tried to focus. He'd file away that remark for later use.

"The levels of the increase eventually steadied out and haven't seemed to give him any troubles. This one is Elizabeth's." Carson frowned.

"It looks the same, so it could be the gene. Carson, are you sure you can't rewire that therapy-"

"Rodney! You of all people should understand what it's like to have someone's voice in your head. Do you really want to go down that road again?"

"Mmm. Right. Look Carson, I need to talk to Sheppard but I wanted your okay because, well, he's not going to be very happy. General O'Neil dialed into get an update from him; Elizabeth has still not rescinded her notice. John's got two days."

John bolted upright in his bed. "_Elizabeth!"_

"What- did he somehow manage to get superman hearing now? That's just great."

"Well you're not exactly quiet Rodney."

Elizabeth rolled over in her bed, turning her back on John. The machines began to tick louder and louder as each of their heart rates and blood pressures rocketed.

"No I will not be quiet, and if you don't quit trying to block me your head is going to explode at some point!" John glanced sideways towards Carson. "Seriously Doc, aspirin."

Carson tore his eyes away from the monitors and headed for the medicine cabinet. McKay hadn't missed the look of concern in his eyes but before he could press Carson he spotted John's movement. The alarms of the monitors seemed to scream as John tugged off all the straps and patches attached to his body. He was off the bed moving towards Elizabeth before Rodney could even try to convince his feet to move. Elizabeth had curled into a ball on her side. John almost hurled himself into the bed with her, pulling her back against his chest.

"I'm sorry Elizabeth, you've got to breathe. Elizabeth breathe, deep breaths." John was talking into her ear, stroking her arms. "You need to calm down. _Elizabeth!_"

Carson stalled dead in his footsteps as he reached Rodney and looked at the monitors. "Bloody hell, I thought it was his, he just ripped off the monitors. Dr. Keller, Elizabeth's gone into cardiac arrest!"

John's eyes were anguished as he looked backward over his shoulder and saw the medical team scrambling. McKay's eyes locked with Sheppard and somehow knew what John was thinking. "Do it." McKay yelled scrambling to grab his computer.

John stretched out pressing his hand to the wall while clutching Elizabeth firmly on the chest with his other hand. McKay frantically scanned through the Atlantian systems looking for it, he suspected-The lights flickered gently before cutting into total darkness.

"Not now, Rodney I have to have lights! Where are the backups?" Carson yelled.

"Elizabeth." John voice cut through the dark, relief obvious in his voice.

The lights snapped back on and McKay grinned; Elizabeth's eyes were fluttering weakly. A nurse shut off John's monitors and the alarm that had resumed was replaced with a constant steady hum of Elizabeth's monitors.

McKay was smiling broadly now as he tapped his computer. He looked up and found Carson with defibrillator in hand, his mouth gaping open. Keller was blinking rapidly but otherwise frozen with her hands on the crash cart. John was whispering in Elizabeth's ear, stroking her hair.

Carson finally laid the defibrillator handles down. "All right, one last time…and I do expect answers this time-what the bloody hell is going on with you two!"

"Carson!" Dr. Keller tilted her head towards him.

Carson sighed and rubbed his hands through his hair. "John, I think I have a pretty good idea of what just happened to her, but I need to run some new tests on Elizabeth. Does this link you two have, can you…communicate only when you are in proximity, in the same room?"

John sat up, his face twisting as he looked down upon Elizabeth. "No."

"_John."_ Elizabeth's voice was weak, but still managed to carry a tone of warning.

John leaned over smiling and gently placed pressed a finger to her lips. "Got to. Look what it just did to you Elizabeth." He looked back at Carson and eased out of the bed. "She's started blocking everything she can and that's tough to do at first. Proximity makes it harder. I need to go, let her rest. You'll keep me posted _right_?"

"All right, but don't think you two are getting off the hook this time. We need to have a serious discussion, that's the only way I'm going to be able to help."

"I might be able to assist with that, I think I know what's going on!" McKay proudly held up his tablet.

---

TBC…


	10. Chapter 10

"Rodney how is it possible that we've never realized it was an artificial intelligence before now?" Carson turned his head towards Rodney as they walked towards Teyla's quarters.

"Because _hello_, it's intelligent." Rodney wondered for the millionth time how it was possible these brilliant people around him always seemed to grasp things so much slower than he did. He supposed they couldn't all be geniuses like himself. He smiled sadly towards his friend before explaining. "We've been running down energy surges all over Atlantis since we've arrived. It was hiding, constantly moving about and drawing energy from different sources quite efficiently masking itself from detection. Obviously, it will only communicate with those with the gene…and apparently those with the highest occurrences of the gene."

"And the energy surges? " Carson's eyebrows furrowed in concentration.

"I'm assuming the program normally only requires a minimal amount of power, nothing we'd ever notice. I think the surges have only occurred when it was mad at Sheppard. Sheppard doesn't understand the Ancient language; he probably thought he was crazy at first, but eventually he managed to just block it out. Can you imagine how mad you would be if no one would talk to you after being alone for 10,000 years?"

"Well I suppose it wasn't entirely alone, the stasis pod-"

"Yes, exactly." Rodney snapped his fingers rapidly before jabbing his pointer finger into the air as he mulled over the probabilities. "It probably connected with the other Elizabeth through the pod. After all those years, we could assume that Atlantis had grown quite fond of Elizabeth. I'd also say it's safe to bet that even if John could block Atlantis, Atlantis could probably still connect with him, especially when he's touching Atlantis. The more contact they have, the stronger the link. Atlantis knew Elizabeth was leaving, and created the gene therapy and the neural link to persuade her to stay. Or more likely finished it in time, it's probably been working on it since the other Elizabeth died."

"Rodney, are you sure about all of this?"

"Carson, I've been running tests for days, since I first noticed the lights flickering when Sheppard touched the wall. There have been huge energy spikes coming from the systems in the lab with the stasis pod. I guess the AI has gotten comfy there or just doesn't care anymore if we figure it out. I compared the times of the power spikes to the irregularities. A perfect match every time. The energy surges have been stronger and stronger. Yesterday's little miracle in the infirmary- the energy spike was off the charts in that moment."

"I wonder if the gene functions somewhat like nanites. That would explain how the surge channeled precisely to jolt Elizabeth's heart. Regardless, if you're right, I hope this will help. She's pushing herself to the max trying to block her link and if she doesn't learn to deal with it quickly, I honestly don't know how much longer she can keep it up. The gene's not natural in her, the link is artificial." Carson's footsteps stalled as the frown deepened on his face. "She's going to have to work harder than John did to get a grasp on this or…"

Rodney stopped as well; he was fully aware his heart rate was creeping upward. "_Or_? What do you mean _or_- that doesn't sound good."

"Well you saw what happened to her, it's too much strain on her body. Her systems will continue to fail if we can't figure out a way for her to deal with this _or_…"

"Carson, will you stop leaving me hanging, you don't have to be so melodramatic!" Rodney waved his hands in the air, growing impatient to get Caron's full attention.

Carson rolled his eyes. "Don't you get it Rodney, she'll _have_ to leave. She won't be able to stay on Atlantis. It'll kill her."

"Ohh." Not good, not good, not good. Elizabeth couldn't leave, he actually _liked_ her, considerably actually, and he'd almost never liked his supervisors in the past. Even more, she was one of the few superiors he'd ever had that tolerated and possibly even understood his theatrics. He couldn't help it if his emotions often got the better of him, showing emotion was supposed to be a good thing, that's what his therapist had told him anyway. McKay started walking now even more determined than before, his finger jabbed the air for emphasis. "This will work. Trust me."

"Ancients also spoke the language we do today. Why hasn't it altered its approach towards communication with John?" Carson jogged a few steps to catch up.

"Hmm. Well, it's an AI, so maybe it only knows the language it was programmed with. Sheppard finally told me he could _see_ Elizabeth in the research lab doubled over in pain, like an image on his mind. Maybe the AI can see what Sheppard sees, saw Elizabeth's packed boxes and figured out what was going on." They reached the transport and Rodney lost himself for a moment pondering Carson's question.

"Rodney?" Carson roused his attention; the transport door was standing open before them.

"Right." He followed Carson inside. The doors whooshed shut. "Ahh, anyway, it would make sense as a security measure. If someone couldn't speak Ancient, well, that probably wouldn't have been anyone the Atlantians wanted the AI to communicate with. Remember, I only said I _thought_ I knew what was going on, that doesn't mean I know every little detail about how and why yet. Though it seems apparent that the AI has grown impatient and it has no qualms about letting them know when it's not happy. Ignoring it is only going to make things worse. We can't afford the power it's drawing when it's demanding John and Elizabeth's attention. "

Carson nudged Rodney again as the transport doors opened. Rodney was hardly even aware of his feet moving out of the transport and down the corridor. His thoughts had been racing so rampantly he could hardly stay in control long enough to make any sense of them. The most recurrent thought running through his mind was almost a reminder; he _had _to take the time to grasp the Ancient language. If Carson could re-create what had happened to Elizabeth and Rodney could establish a link of his own with Atlantis, oh that would be unbelievable!

"Rodney, it's an AI- it's not supposed to have feelings." Carson's voice jolted him from his reverie.

"Says who? This is Ancient technology, we have no idea how it was programmed. It seems obvious that it's adapted, it's learning, changing its approach to communication. We need to get Elizabeth to stop fighting this and actively try to listen and talk to it if we're to find out anything more. Because if we ignore it…well, if it's anywhere near as stubborn as John and Elizabeth anyway, it'll deplete so much power we'll lose the ability to shield Atlantis. And that would just be the beginning."

"But it helped Elizabeth." Carson frowned.

"I _know_ that Carson, I'm the one that told John to try. Okay, now just imagine how much help it could be if we were actively communicating with it on a regular basis? It could help us find more Zed PM's, explain what's in all the unexplored areas of Atlantis, who knows what kind of gold mines we're potentially sitting on! It could tell us what systems may need repairing, help us strengthen sensors, distribute power more efficiently… the possibilities are endless!" His heart thumped louder with every footstep, it actually hadn't quit racing since he'd first figured out they could communicate with Atlantis. There were so many hours he'd personally potentially wasted trying to wrap his mind around Atlantian systems that had John only understood the Ancient language they could have simply asked the AI. Unbelievable.

"Finally." Carson muttered.

Rodney peered up and spotted Teyla standing outside the doors to her quarters speaking with John.

"Will you give us a minute Teyla?'' John asked. He looked almost as pitiful as a schoolboy just sentenced to detention.

She nodded silently and stepped aside. Rodney upped his pace wondering if she'd gone mad as John entered the room where Elizabeth waited. Surprisingly, it had been Elizabeth who'd protested the most over Carson's insistence that John continue to stay away from her during the past twenty four hours. It was only because Elizabeth's blood pressure had risen higher every hour after John left the infirmary combined with her inability to sleep, even under medication, that Carson had agreed to this now.

Teyla turned towards Rodney and Carson effectively blocking the doorway when she crossed her arms. "Trust him, trust them both. They have to resolve this with each other before they can attempt to do what you ask."

The men offered no resistance and she turned back towards the candlelit interior of her quarters. The three peered cautiously through the doorway. Elizabeth was adorned in her yoga gear, her back towards them as she rested with her left shoulder against the wall. John paused a few footsteps into the room. Silence hung painfully in the air; Rodney found himself holding his breath afraid to make any noise. Elizabeth and John stood rigid and unmoving. Rodney couldn't even fathom a guess if the two were fighting, declaring a truce, or even speaking at all. John started turning back towards them and the three twisted out of the doorway planting their backs against the wall.

"This is ridiculous, why are we hiding?" Rodney hissed.

Teyla turned to stand on her tiptoes stretching her head above Rodney's as Carson crouched down lower. Their three heads cautiously peeked back around the entryway.

John had turned again, headed swiftly back towards Elizabeth. He tucked in behind her, his right hand tentatively daring to rest upon her shoulder. Another breath holding, patience testing moment passed before Rodney spotted Elizabeth's left hand cross her body. Her fingers crept up to her shoulder slowly intertwining with John's. She tilted her head back towards him and the look that passed between John and Elizabeth was poignant enough to make Rodney's own heart jolt in response. He'd reluctantly accepted the idea of them before, but now he found himself cheering them on hoping…John's head tilted down brushing his lips against Elizabeth's.

Rodney couldn't suppress his exuberant "Ohh…." from escaping.

"Rodney!" Teyla admonished.

Rodney would have sworn he heard a soft growl rumbling in John's throat when he pulled away from Elizabeth. Their eyes darted around towards the sounds that had emerged from the doorway. Rodney smiled weakly and waved. John's eyes were dark as he pivoted around, moving Elizabeth with him. It didn't escape Rodney how Elizabeth trusted John with her weight as she nestled back against his chest. John wrapped his arms possessively around her waist; his eyes rang with silent warning, almost daring Carson to try to separate them again.

"Teyla, we're ready." Elizabeth's voice resonated stronger than Rodney had heard it in days. She seemed unusually content within John's arms, the tension had fallen away from her shoulders and the corners of her eyes crinkled as a soft smile crept across her face.

Teyla was tugging his hand; Rodney turned in surprise and found she held Carson's hand as well. She led them firmly back into the corridor. "Your presence is not necessary. I will try my best, but I do not make any promises that meditating will strengthen their ability to communicate with Atlantis."

"Don't worry about that Teyla, the bond is there, no doubt about it. Elizabeth just has to open up to it, trust it, and talk to it again. Will you let us know when you've finished? We'll need to talk to them." Rodney was almost drooling at the thought of the information they could recover tonight.

Teyla moved closer, her eyebrow arched high in warning. "It is late. If it works as you hope, they will need to rest. We have lived without the assistance of this…artificial intelligence for a long time. You can wait until morning, I am sure Dr. Beckett will agree."

"She's right Rodney; we can't push them, especially Elizabeth. Teyla, make sure she uses the monitor I sent down, I've got a team on standby if-"

"I know what to do Dr. Beckett. " Teyla left them and moved back into her quarters.

"Teyla?" Carson called. "Good luck."

Rodney looked beyond Teyla and saw John's eyes radiating as he looked at Elizabeth. She was facing him now, her palm gently resting on his forearm. Rodney's chest puffed with something other than pride and he felt somewhat unsettled as he watched his friends. It wasn't pride, wasn't even jealously. Rodney realized that he was simply touched by what his friends had managed to find within each other. He was…happy for them.

He shook it off ambling away with Carson while trying to suppress his forming frown. It was quite possible he'd spent entirely too much time on Atlantis. He was becoming soft. He felt the corners of his lips begin to lift again. He considered the possibility that perhaps it was the friendships he'd forged on Atlantis. Their steady support had been quietly transforming him into a better man. They were all transforming into better versions of themselves.

Rodney turned back one more time, Elizabeth and John were sitting cross legged in front of each other as Teyla guided them into meditation. Elizabeth's hands snaked out latching onto John's; John's hands squeezed hers tightly in response. Their foreheads came to rest against each other's and the lights in the room flickered gently as if in approval.

Rodney thought of the letter he'd written to Samantha before he'd left for Atlantis. In a rare sappy I could possibly die tomorrow kind of moment, he'd dug up the quote "Two people, two hearts, two lives, become one heart, one mind, one new life together." His chest again constricted strangely. He realized he'd just been privileged to witness that very moment of acceptance within his friend's hearts.

Rodney turned around and resolved to finally send that damn letter to Sam the next time the Deadalus was on Atlantis. With any luck, General O'Neil wouldn't kill him. After seeing Elizabeth and John together tonight, he had to try. The odds were against him, humiliation probable, but nothing could scare him now, nothing except the thought of passing by a chance to find what he'd witnessed his friends share. If it couldn't be Sam, well, he felt certain the next time he felt that flicker stir within his heart, he'd remember tonight again and chase it with everything he had within him.

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TBC- Thanks for the reviews and story alerts. More on the way…


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